CHICO — For more than 60 years, salmon have been cut off from the San Joaquin River.

Dams were built and riverbeds went dry. Lawsuits ensued.

Now a massive plan to restore fish habitat is under way, perhaps the largest of its kind ever attempted. The goal is also to bring back the fall- and spring-run chinook salmon, as well as other fish.

The Feather River Fish Hatchery in Oroville will play a key role, by producing fish for transport to the San Joaquin.

The target timeline for fish release is 2016.

Representatives from state and federal agencies that work with fish were in Chico Tuesday for an update on the project, which will include restoring land along the San Joaquin River, putting water back into the river, and eventually a hatch-and-release program.

Rhonda Reed of the National Marine Fisheries Service gave a similar presentation in Chico last May, as well as in February 2011.

Originally, one of the ideas was to collect fish from several different waterways, including the four creeks in Northern California where salmon still naturally migrate and spawn.

But that idea has been shelved for now.

Burt Bundy of the Mill Creek Conservancy said it has been a struggle for the populations of salmon in Mill Creek, which runs from Lassen Peak to the Sacramento River. At times, spring-run chinook have been as low as a few hundred.

"If you take fish, I want to make sure they survive," Bundy said.

Reed said the plan in the works only includes hatchery fish. However, fish scientists believe the fish would have the best chance of survival if they have genetics from a variety of locations, including natural spawners from creeks.

The plan to take fish from the hatchery must ensure that the project will not harm the fish population in other areas, said Elif Fehm-Sullivan of the Fisheries Service.

Another question raised this week was about fishing in the future, if spring and fall-run salmon are re-established in the San Joaquin River. Steve Carson, fishing enthusiast, said he'd like to see guidelines in the document for when fishing could resume. But Carson said he also understood that would be after fish populations increased.

Reed said ideally, fishing would be allowed some day, but the first step is to get the fish in the river, and watch to see if they thrive.

"We're using the hatchery facility so we can get to the reintroduction goals in the San Joaquin by increasing the numbers in the hatchery," Reed said.

Parts of the San Joaquin River have been dry for more than 60 years due to the Friant Dam near Fresno, which provides irrigation water in the San Joaquin Valley.

In 1988, the U.S. Department of Interior was in negotiation to renew the water contract for Friant Dam. The National Resources Defense Council and a coalition of others challenged the renewal in court.

The group argued California Fish and Game codes require dams to release enough water to keep fish in good condition downstream, according to a report online at http://restoresjr.net.

That had not happened, because all the water had been diverted to irrigation canals.

In 2006, a settlement was reached, and now a plan has evolved to restore water to the river.

The settlement requires water releases from Friant Dam to where the river meets the Merced River. Flows vary between about 247,000 acre-feet in dry years to about 555,000 acre-feet in wet years.

One acre-foot is 325,851 gallons, and enough water to cover 1 acre of land at a foot deep.

Another point that has taken time to work out is protections for water users along the San Joaquin River.

Water users were worried that if endangered spring-run chinook salmon are reintroduced to the river, water users could face penalties if endangered fish are harmed through normal water use, including water pumps.

Over the past several years, the project has worked to ensure that the fish released will be officially an "experimental" population, and not subject to the same environmental protection rules. This would apply upstream from the Merced River, explained Rhonda Reed during the workshop in Chico Tuesday.

Working all of those details out has taken several years.

Agencies working on the project include the U.S. Fish and Wildlife Service, the Fisheries Service and California Fish and Wildlife.

Staff writer Heather Hacking can be reached at 896-7758, hhacking@chicoer.com, and followed on Twitter @HeatherHacking.